i have my new OS instalation on a new disk... the old one is in slaved inside the box so i can copy back the sites files... is there a way to copy the full stuff of a user? like... sites, email, email addresses, mysql databases etc etc ?

for the mysql databases i am copying the files in /var/lib/mysql/dbname from one disk to the the other... but inside phpmyadmin it says the table are "in use" and wont work

cpanel has a built in backup and restore script which will put everything back in its place automatically. It looks like you weren't using it and will need to put everything back manually. The cpanel way takes about 4 seconds to do but the manual way takes much longer.